Microarray profiling analysis of whole transcriptome expression in osteosarcoma
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PROVIDER: PRJNA936576 | ENA |
REPOSITORIES: ENA
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Project description:Osteosarcoma (OS)is a rare primary malignant bone tumor in adolescents and children with a poor prognosis. Identification of prognostic genes lags far behind the advance of the treatments. We identified differential genes by microarray analysis from paired OS tissues. Hub genes, gene set enrichment analysis, and pathway analysis were performed to gain an insight into the pathway alterations of OS. These results showed CPE could be served as a prognostic factor in osteoblastic OS and should be further investigated as potential therapeutic target. The present study evaluated the whole transcriptome expression of osteosarcoma progression and provided novel therapeutic targets for advanced osteosarcoma.
2023-03-01 | GSE225588 | GEO
Project description:Microarray profiling analysis ofcircular RNAs expression in osteosarcoma
| PRJNA589051 | ENA
Project description:Strategies targeted vascular endothelial growth factor (VEGF)-dependent osteosarcoma progression are limited although important progress has been made in illustrating the mechanisms. Here we identified circ_001621 as one of the significantly upregulated circular RNAs (circRNAs) by circRNAs microarrays. We found that patients with high circ_001621 expression had a shorter survival time. Moreover, we found several potential sponge micro RNAs (miRNA) of circ_001621 with Circular RNA Interactome database. Among the candidate sponge, we elucidated the association of circ_001621 and miR-578. In addition, we demonstrated that miR-578 targeted circ_001621 directly. Functionally, we set up the experimental system to investigate the effects of circ_001621/miR-578/VEGF interaction in vitro and in vivo. Results indicated circ_001621 promoted osteosarcoma proliferation and migration via attenuating the inhibition of cyclin-dependent kinase 4 (CDK4) and matrix metallopeptidase 9 (MMP9) by miR-578, respectively. Nude mice experiment was further performed to estimate the promotion of metastasis by circ_001621. The present study evaluated the mechanisms underlying circ_001621 enhanced osteosarcoma progression and provided novel therapeutic targets for advanced osteosarcoma. Circular RNAs profiling by array
2020-01-14 | GSE140256 | GEO
Project description:Seven human osteosarcoma cell lines (U2OS, U2OS/MTX300, HOS, MG63, 143B, ZOS, ZOSM) and the human osteoblast hFOB1.19 were included in the study. Microarray based circRNA expression profiles were acquired using the Arraystar Human circRNA Array (8x15K, Arraystar). We identified circRNAs differentially expressed in human osteosarcoma cell lines compared to human osteoblast hFOB1.19 (control).
2017-04-12 | GSE96964 | GEO
Project description:We performed whole transcriptome analysis of osteosarcoma bone samples. Initially we sequenced total RNA from 36 fresh-frozen samples (18 tumoral bone samples and 18 non-tumoral paired samples) matching in pairs for each osteosarcoma patient. We also performed independent gene expression analysis of formalin-fixed paraffin-embedded (FFPE) samples to verify the RNAseq results. The use of FFPE samples allowed to analyse the effect of chemotherapy. Data were analysed with DESeq2 and Reactome packages of R. We found 6775 genes expressed differentially between the normal bone and osteosarcoma tissues with an FDR below 0.1, of which 4092 genes were up-regulated and 2683 were down-regulated. Among those genes, BTNL9, MMP14, ABCA10, ACACB, COL11A1 and PKM2 were expressed differentially with the highest significance between tumor and normal bone. Functional annotation with the Reactome identified significant changes in the pathways related to the extracellular matrix degradation and collagen biosynthesis. Analysis of independent FFPE samples largely verified our findings in fresh frozen samples, indicating that osteosarcoma is characterized by massive bone loss. We also found that chemotherapy induced the bone formation and reverses the bone loss caused by sarcoma. Taken together, our results indicate that changes in the degradation of extracellular matrix seem to be an important mechanism of osteosarcoma and efficient chemotherapy induces the genes related to bone formation.
2017-11-03 | GSE99671 | GEO
Project description:Osteosa rcoma is an aggressive malignant neoplasm that exhibits osteoblastic differentiation and produces malignant osteoid. The aim of this study was to find feature genes associated with osteosarcoma and correlative gene functions which can distinguish cancer tissues from non-tumor tissues. Gene expression profile GSE14359 was downloaded from Gene Expression Omnibus (GEO) database, including 10 osteosarcoma samples and 2 normal samples. The differentially expressed genes (DEGs) between osteosarcoma and normal specimens were identified using limma package of R. DAVID was applied to mine osteosarcoma associated genes and analyze the GO enrichment on gene functions and KEGG pathways. Then, corresponding protein-protein interaction (PPI) network of DEGs was constructed based on the data collected from STRING datasets. Principal component of top10 DEGs and PPI network of top 20 DEGs were further analyzed. Finally, transcription factors were predicted by uploading the two groups of DEGs to TfactS database. A total of 437 genes, including 114 up-regulated genes and 323 down-regulated genes, were filtered as DEGs, of which 46 were associated with osteosarcoma by Disease Module. GO and KEGG pathway enrichment analysis showed that genes mainly affected the process of immune response and the development of skeletal and vascular system. The PPI network analysis elucidated that hemoglobin and histocompatibility proteins and enzymes, which were associated with immune response, were closely associated with osteosarcoma. Transcription factors MYC and SP1 were predicted to be significantly related to osteosarcoma. The discovery of gene functions and transcription factors has the potential to use in clinic for diagnosis of osteosarcoma in future. In addition, it will pave the way to studying mechanism and effective therapies for osteosarcoma.
| S-EPMC4565213 | biostudies-literature
Project description:Cross species transcriptome analysis of osteosarcoma
| PRJNA345550 | ENA
Project description:Osteosarcoma is a form of bone cancer that predominantly impacts osteoblasts, the cells responsible for creating fresh bone tissue. Typical indications include bone pain, inflammation, sensitivity, mobility constraints, and fractures. Utilizing imaging techniques such as X-rays, MRI scans, and CT scans can provide insights into the size and location of the tumor. Additionally, a biopsy is employed to confirm the diagnosis. Analyzing genes with distinct expression patterns unique to osteosarcoma can be valuable for early detection and the development of effective treatment approaches. In this research, we conducted a comprehensive examination of the entire transcriptome and pinpointed genes with altered expression profiles specific to osteosarcoma.The study mainly aimed to identify the molecular fingerprint of osteosarcoma. In this study, we processed a total of 90 FFPE samples from PathWest of which 45 were OS and equal number of healthy tissues. RNA was extracted from Paraffin-embedded tissue; RNA was sequenced, the sequencing data was analysed and gene expression was compared to healthy of the same patients. Differentially expressed genes in osteosarcoma derived samples were identified and the functions of those genes were explored. This result was combined to perform meta-analysis with our previous studies based on FFPE and fresh samples. We identified 1,500 identical differentially expressed genes in PathWest osteosarcoma samples when compared with normal tissue sample of the same patients. Meta-analysis with combined fresh issue samples identified 504 differentially expressed genes. IFITM5, MMP13, PANX3, MAGEA6 were some of the most overexpressed genes in osteosarcoma samples while SLC4A1, HBA1, HBB, AQP7 genes were some of the top downregulated genes. Through the metanalysis, 504 differentially expressed genes were identified to be identical among FFPE (105 FFPE samples) and 36 fresh bone samples. These 504 differentially expressed genes can be taken as a molecular fingerprint of osteosarcoma.
2024-07-10 | GSE253548 | GEO
Project description:Osteosarcoma is a rare, highly malignant tumor of the bone that presents with a highly complex and abnormal karyotype. Only a few of the genes, which are targets of genetic alteration are known. An integrated genome-wide genomic and gene expression profiling analysis was performed on human osteosarcoma tissues and osteosarcoma cell lines in order to identify and map, in a high-resolution fashion, the most drastic chromosomal changes and point out genes which could contribute to tumorigenesis by having altered expression levels of critical oncogenes and tumor suppressors. Combined gene expression and aCGH analysis on the same samples enables direct comparison between DNA and mRNA level and offers a general strategy to identify and prioritize potential targets while the parallel analysis on cell lines offers a reliable models for further functional studies.
2016-01-01 | GSE12512 | GEO
Project description:Osteosarcoma is the most common primary bone cancer in children, adolescents and young adults. It is a rare cancer type. To comprehensively reveal the transcriptomic characteristics of osteosarcoma, we performed Oxford Nanopore Technologies (ONT) long-read RNA-Seq of tumor and adjacent normal tissues from 23 patients with osteosarcoma.
2023-07-19 | GSE218035 | GEO